Increased accessibility of bases in DNA upon binding of acridine orange.

Acridine orange (AO) forms 1:1 complexes with dsDNA which are insoluble in aqueous media, exhibit red luminescence, have minimal green luminescence and resemble complexes of AO with ss nucleic acids. During formation and/or dissociation of these complexes, accessibility of DNA bases to two conformational probes, formaldehyde and diethyl pyrocarbonate is increased, suggesting that the base pairing is destroyed and DNA at least partially denatured. Adriamycin and Ellipticine, but not Ethidium Bromide exert similar destabilizing effects. The results confirm our earlier predictions based on thermodynamic calculations that the double helix undergoes destabilization upon binding an intercalator characterized by high cooperativity in interaction with ss nucleic acids. Thus, the highly cooperative ligand binding to ss sections during the "breathing" of the polymer may progressively destabilize the adjacent ds structure.     

Acridine orange distribution and fluorescence spectra in myoblasts and single muscle fibers

Acridine orange (AO) fluorescence spectra in nuclei and cytoplasm of living myoblasts L6J1 and frog single muscle fibers have been studied using spectral scanning system of Leica TCS SL confocal microscope. AO fluorescence spectra in salt solutions dependent on free AO concentrations or in complex with DNA have also been obtained. Myoblast nuclei fluoresced in the green spectral region with maximum at about 530 nm; nucleoli had the brightest fluorescence. The fluorescence of nuclear chromatin was not uniform. Similar fluorescence of nuclei and nucleoli was observed in frog single muscle fibers. Uniform, weak, green fluorescence was observed in the myoblast cytoplasm. In the sarcoplasm of muscle fibers, AO green fluorescence was seen in A discs. In the cytoplasm of myoblasts and muscle fibers stained with AO, different red, yellow, and green fluorescent granules, which were acidic organelles, were visualized. The comparison of AO fluorescence spectra in living cells with AO fluorescence spectra in buffer solutions with different AO concentrations and AO in complex with DNA enables the estimation of the AO concentration in acidic granules. It is important for the evaluation of these cellular organelles functions in intracellular transport, adaptation, and apoptosis, as well as in a number of pathological processes.     

Increase in acridine orange (AO) fluorescence intensity of monocytes cultured in plastic tissue culture plates as measured by flow cytometry.

Although the green-red fluorescence of AO is an accepted measure of DNA-RNA content, respectively, it is actually a measure of the fluorescence of dye bound to nucleic acids, and may vary with changes in accessibility to the dye. It has been shown for example that extraction of nuclear proteins results in a marked increase in DNA stainability. Moreover, in certain cell systems the binding of fluorochromes correlates with structural modifications in chromatin that accompany cell differentiation. We report here that changes in green & red fluorescence intensity also occur in long-term monocyte cultures. The increased red fluorescence intensity observed in cultured monocytes may reflect ribosomal RNA synthesis and the increased green fluorescence enhanced AO accessibility to DNA due to changes in chromatin organization. We compared cultured monocytes from bladder cancer patients and healthy donors. The results indicate a small but statistically significantly greater increase in mean green & red fluorescence of cultured monocytes from the cancer patients. These fluorescence variations may indicate differences in the immunologic status of cancer patients and/or be related to disease state.     

A Color Image Analysis Method for Assessment of Germination Based on Differential Fluorescence Staining of Bacterial Spores and Vegetative Cells Using Acridine Orange

Color fluorescence image analysis of acridine orange (AO) stained germinating Bacillus subtilis var. niger bacteria revealed a cell population initially dominated by small green spores followed by the emergence of at least three additional discernible subpopulations in response to stimulation with D-glucose. These subpopulations were small, round or oblong red cells; intermediate to large metachromatic cells; and large red rods. Large green rods were rarely observed. An increase in red emissions (i.e., putative RNA synthesis) was sometimes seen as early as 90 min after exposure to D-glucose and uptake of AO at room temperature. This may represent either metabolic recovery from quiescence or RNA synthesis associated with germination. In the absence of D-glucose, or using autoclaved bacteria in the presence of glucose, no relative increase in the red signal was observed despite hours of observation. Digital image analysis was used for relative measurement of red, green and blue signals and to correlate the size of various subpopulations with their fluorescence color emissions over time. Image analysis demonstrated a trend toward increasing size and red emission in the presence of glucose. The average red emission was found to be a good discriminator of the various subpopulations, while the average green emission was approximately equal among the subpopulations making it a poor discriminator. These data suggest that AO staining might be used for rapid computer-assisted discrimination of spores vs. vegetative cells.     

Molecular Complexes of acridine orange and nucleosides

Summary The addition of various nucleosides to the aqueous AO solution brings about the red shift of the absorption band of AO monomer and the enhancement of the AO fluorescence emission. These phenomena are attributable to the formation of a kind of molecular complex between AO monomer and nucleoside.The absorption and fluorescence characteristics and their thermal behaviours enable us to determine the association constant and the binding energy. The binding energy of AO with purines is larger than that with pyrimidines, and the association constant between AO and the deoxyribonucleoside is larger than that between AO and the ribonucleoside. For the molecular complexes dealt with, the face-to-face arrangement of AO and nucleoside, linking of AO with sugar by hydrogen bridge, may be more preferential than the side-by-side arrangement with the direct linkage between AO and nucleic acid base by hydrogen bonding. The Van der Waals-London interactions may be one of the essential factors for the binding in these molecular complexes.The association constant and the binding energy for AO-DNA and -RNA systems were also determined. The magnitude of these quantities seems to reflect the difference in the structure of these nucleic acids. The rather open structure of RNA compared with DNA is in favour of affinity with AO and gives the larger association constant than that for AO-DNA. The binding energy is somewhat larger for AO-DNA complex than for AO-RNA complex, probably due to the structural difference of the base arrangement; the stacked base pairs for DNA and the stacked bases for RNA.This may explain the selective degradation [12] of guanine photo-sensitized by dyes either in the free state or when incorporated to DNA or RNA, as discussed elsewhere.     

Improved flow cytometry of cellular DNA and RNA by on-line reagent addition

Acridine orange (AO) staining enables flow cytometric measurement of cellular DNA and RNA. With the conventional procedure, red and green fluorescence intensities alter considerably in time, affecting the reliability and reproducibility of the results. A standardized simple technique of AO staining is described that keeps the time between addition of detergent and AO and the subsequent measurement constant. Measurements by means of this on-line method appear to be much more reproducible in comparison to those obtained using the conventional procedure.     

A scene-segmentation method for multispectral cell images

A scene-segmentation method for two-color digitized images acquired from a Papanicolaou-stained cervical smear is proposed. The method first segments a scene into background, red cytoplasm, blue cytoplasm and nuclear regions by a pixel-wise classification and then merges the segmented regions for both types of cytoplasm into a single region. To create the minimum-distance classifier used for the pixel classification, class median vectors are selected from a two-dimensional histogram formed from the optical densities in the red and green images (scanned at 610 nm and 535 nm, respectively). Reference points defined from knowledge about the two-color images played an important role in selecting the vectors for the red and blue cytoplasm. This method was applied to 33 sets of the two-color images. The resulting segmented regions corresponded well with regions apparent to the the human observer. Three different investigations related to the method were carried out; these studies confirmed the suitability of the proposed method.     

The anatomy of a range expansion: changes in cranial morphology and rates of energy extraction for North American red squirrels from different latitudes

Species with expanding ranges provide unique opportunities to examine environmentally induced adaptations in ecological traits and anatomical characteristics. Since the late 1800s, the North American red squirrel (Tamiasciurus hudsonicus) has expanded its range into the central hardwoods of the United States in conjunction with increasing agricultural fragmentation. We examined whether red squirrels from the central hardwoods (west‐central Indiana, USA) displayed differences in foraging behaviors and morphology relative to red squirrels from conifer‐dominated environments (upper peninsula of Michigan, USA), a biome in which red squirrels evolved. Specifically, we measured rates of energy extraction, variation in cranial morphology, and diet preference between red squirrels from both regions. In addition, we compared foraging behaviors of red squirrels from the central hardwoods to those of a competitor that coevolved with nut‐producing trees, the gray squirrel (Sciurus carolinensis). Red squirrels from Indiana and Michigan differed significantly in the efficiency with which they used food items, with individuals from each region extracting calories at a more rapid rate for items that were common in their region. The enhanced efficiency of southern red squirrels feeding on black walnuts (Juglans nigra) was correlated with geographic differences in cranial morphology; skulls of southern squirrels were larger, with longer jaws and higher metrics associated with greater mandibular force than northern squirrels. Contrary to our expectations, red squirrels from Indiana and Michigan did not differ qualitatively in preferences for food items, suggesting that diet choice may be governed by perishability of food items rather than by rates of energy extraction. Gray squirrels were more efficient than Indiana red squirrels in using all food items, and differed only slightly from red squirrels with regard to preference for food items. Measures of efficiency of resource use, after accounting for species‐specific metabolic requirements, suggest that red squirrels are unlikely to compensate ecologically for declining gray squirrel populations in fragmented portions of the central hardwoods, with potentially adverse effects for forest regeneration and succession. Our results demonstrate that invading species can display significant flexibility in adapting to new environments, but they may not be flexible enough to exploit resources in a manner comparable to native species.     

Denaturation and condensation of DNA in situ induced by acridine orange in relation to chromatin changes during growth and differentiation of Friend erythroleukemia cells

DNA in situ is progressively denatured when the cells or nuclei are treated with increasing concentration of acridine orange (AO). This transition can be monitored by flow cytometry as a decrease in green fluorescence. The complexes of denatured DNA and AO undergo immediate condensation and aggregation; this step is manifested by appearance of red luminescence and formation of precipitates that can be detected by electron microscopy. The precipitates form preferentially in heterochromatin as well as in ribosomes and polysomes. Their formation and further aggregation affects cellular light scatter properties in both the forward and right-angle direction. The AO-induced DNA denaturation and condensation was studied in nuclei of Friend erythroleukemia cells from exponentially growing, differentiated or quiescent cells. The DNA in nuclei of quiescent cells, from plateau-phase cultures, was the most sensitive to denaturation; it denatured (measured by changes in luminescence) at an AO concentration between 50 and 80 microM with the midpoint of the transition (Cd) at 70 microM. DNA in nuclei of differentiated cells (dimethyl-sulfoxide-induced erythroid differentiation) was more resistant (Cd = 77-83 microM), whereas DNA in exponentially growing cells was the most resistant (Cd = 86 microM). Extraction of proteins with 0.1 M HCl at 0 degree C abolished the differences between the cells and shifted the transition to a lower AO concentration (Cd = 46 microM). For comparison, the midpoint transitions representing condensation of free, nucleic acids measured as light scatter changes occurred at 13, 22, 31 and 53 microM of AO, for rRNA, tRNA, and denatured and native-calf thymus DNA, respectively. Denaturation and condensation of DNA, which can be induced by AO either in isolated nuclei or viable permeabilized or fixed cells provides a new approach to discriminate cell subpopulations with different chromatin structure by flow cytometry. The molecular mechanisms of this phenomenon are discussed.     

Mutagenesis of apobec-1 complementation factor reveals distinct domains that modulate RNA binding, protein-protein interaction with apobec-1, and complementation of C to U RNA-editing activity

C to U editing of apolipoprotein B (apoB) RNA requires a multicomponent holoenzyme complex in which minimal constituents include apobec-1 and apobec-1 complementation factor (ACF). We have examined the predicted functional domains in ACF in binding apoB RNA, interaction with apobec-1, and complementation of RNA editing. We demonstrate that apoB RNA binding and apobec-1-interacting domains are defined by two partially overlapping regions containing the NH(2)-terminal RNA recognition motifs of ACF. Both apoB RNA binding and apobec-1 interaction are required for editing complementation activity. ACF is a nuclear protein that upon cotransfection with apobec-1 results in nuclear colocalization and redistribution of apobec-1 from the cytoplasm. ACF constructs with deletions or mutations in the putative nuclear localization signal (NLS) still localize in the nucleus of transfected cells but do not colocalize with apobec-1, the latter remaining predominantly cytoplasmic. These observations suggest that the putative NLS motif in ACF is not responsible for its nucleo-cytoplasmic trafficking. By contrast, protein-protein interaction is important for the nuclear import of apobec-1. Taken together, these data suggest that functional complementation of C to U RNA editing by apobec-1 involves the NH(2)-terminal 380 residues of ACF.     

Conformational studies of Escherichia coli ribosomes with the use of acridine orange as a probe

The interaction of E. coli vacant ribosomes with acridine orange (AO) was studied, to obtain conformational information about rRNAs in ribosomes. Acridine orange binds to an RNA in two different modes: cooperative outside binding with stacking of bound AO's and intercalation between nucleotide bases. Free 16S and 23S rRNAs have almost identical affinities to AO. At 1 mM Mg2+, AO can achieve stacking binding on about 40% of rRNA phosphate groups. The number of stacking binding sites falls to about 1/3 in the 30S subunit in comparison with free 16S rRNA. In the 50S subunit, the number of stacking binding sites is only 1/5 in comparison with free 23S rRNA. Mg2+ ions are more inhibitory for the binding of AO to ribosomes than to free rRNAs. The strength of stacking binding appears to be more markedly reduced by Mg2+ in active ribosomes than in rRNAs. "Tight couple" 70S particles are less accessible for stacking binding than free subunits. The 30S subunits that have irreversibly lost the capability for 70S formation under low Mg2+ conditions have an affinity to AO that is very different from that of active 30S but similar to that of free rRNA, though the number of stacking binding sites is little changed by the inactivation. 70S and 30S ribosomes with stacking bound AO's have normal sedimentation constants, but the 50S subunits reversibly form aggregates.     

Rapid assessment of islet viability with acridine orange and propidium iodide

Summary A simple, rapid method for estimating the viability of isolated islets of Langerhans with fluorescent dyes is described. Low concentrations of acridine orange and propidium iodide (AO/PI) were used to visualize living and dead islet cells simultaneously. AO/PI-stained islets can be divided into three distinct groups. Group A islets fluoresce green, contain insulin, and have normal ultrastructure; group C islets fluoresce primarily red, contain little or no insulin, and have cells with disrupted cellular membranes. Group B islets fluoresce red, green, and yellow. The yellow color is due to the addition of two primary colors from the superimposed red and green fluorescing cells. In this assay, the interpretation that red islet cells are dead and green islet cells are alive was confirmed by sequentially staining single islet cells with AO/PI and trypan blue. The observation that red islets are dead was confirmed by heat-killing, enzymatically damaging, treating with ethanol, or depriving islets of nutrients and observing the red fluorescence. This assay should be useful in studies where the assessment of islet viability is essential. Preliminary reports of this work were presented at two meetings and were published in abstract form (24,25). This research was supported in part by the National Institutes of Health, Bethesda, MD, grant DK 18115.     

Study of the structural organization of RNA from phage MS2 using fluorescent dyes

The spatial organization of phage MS2 RNA by binding to ethidium bromide (EtBr) and acridine orange (AO) to RNA was studied. The analyses of dye interaction by spectrophotometric and fluorometric methods have demonstrated that only about a half of 65-70% nucleotides of double-stranded segments can interact with AO and EtBr. On the other hand all the single-stranded segments appear to be accessible to AO binding. These interactions did not practically change when ionic strength (0.01-0.3), Mg2+ and Zn2+ concentrations (10(-3) M) or pH (4.7-7.4) varied. The data permit to suppose that phage MS2 RNA has a very stable tertiary structure which makes part of double-stranded segments unaccessible to inter calating dyes. Taking these and other facts into consideration we suppose that double-stranded segments play an important role in stabilization of the RNA tertiary structure. One of the most possible structure is a compact "rod-like" intramolecular aggregate of double-stranded hairpin-like segments of RNA with parallel orientation.     

The Mechanism of Replacement of Red Squirrels by Grey Squirrels: A Test of the Interference Competition Hypothesis

Introduced American grey squirrels have replaced native red squirrels in most of the range currently occupied in Britain and northern Italy. The mechanisms of the replacement are not yet fully understood. We restated the commonly cited Interference Competition Hypothesis (ICH) that grey squirrels interfere with the behaviour of red squirrels in three possible ways: 1. by direct aggressive interactions; 2. by interrupting red squirrel mating-chases; or 3. by forcing red squirrels to actively avoid areas intensively used by grey squirrels. We compared the activity pattern, behaviour and reproductive performance of red squirrels in two study areas in northern Italy, one with only red squirrels (control area C1), the other with both species (experimental area E1). The following predictions were tested: 1. the total time spent in both intraspecific and interspecific interactions by red squirrels increases in the experimental area; 2. most interspecific interactions are aggressive, with grey squirrels being the dominant species; 3. the proportion of breeding female red squirrels that are unsuccessful at weaning offspring increases in area E1; 4. grey squirrels take part and interfere with red squirrel mating-chases, and thereby decrease the reproductive output of red squirrel females; 5. the activity pattern of red squirrels in the mixed-species area is shifted with respect to that in the control area to the hours of the day during which grey squirrels show little activity; and 6. red squirrels will shift their home range (or at least their core-area) when grey squirrel densities increase to avoid interspecific core-area overlap. Our results supported only the first prediction of the ICH: they failed to support all the other predictions. Moreover, the increase in the percentage of active time red squirrels spent interacting with other squirrels in the experimental study area was very small (only 1–2 min/day). Red squirrels did not avoid the woodland patches most intensively used by grey squirrels and the interspecific core-area overlap was similar to red squirrel intraspecific core-area overlap. This suggested that red squirrels avoided spatial overlap with grey squirrels in a similar manner as with conspecifics and that an increase in grey squirrel numbers will augment the intensity of resource competition. We therefore conclude that our results do not lend support to the Interference Competition Hypothesis and that interference competition by grey squirrels cannot explain the large-scale replacement of red by grey squirrels that has occurred in Britain and in Piedmont.     

Systematic colocalization errors between acridine orange and EGFP in astrocyte vesicular organelles

Dual-color imaging of acridine orange (AO) and EGFP fused to a vesicular glutamate transporter or the vesicle-associated membrane proteins 2 or 3 has been used to visualize a supposedly well-defined subpopulation of glutamatergic astrocytic secretory vesicles undergoing regulated exocytosis. However, AO metachromasy results in the concomitant emission of green and red fluorescence from AO-stained tissue. Therefore, the question arises whether AO and EGFP fluorescence can be distinguished reliably. We used evanescent-field imaging with spectral fluorescence detection as well as fluorescence lifetime imaging microscopy to demonstrate that green fluorescent AO monomers inevitably coexist with red fluorescing AO dimers, at the level of single astroglial vesicles. The green monomer emission spectrally overlaps with that of EGFP and produces a false apparent colocalization on dual-color images. On fluorophore abundance maps calculated from spectrally resolved and unmixed single-vesicle spectral image stacks, EGFP is obscured by the strong green monomer fluorescence, precluding the detection of EGFP. Hence, extreme caution is required when deriving quantitative colocalization information from images of dim fluorescing EGFP-tagged organelles colabeled with bright and broadly emitting dyes like AO. We finally introduce FM4-64/EGFP dual-color imaging as a remedy for imaging a distinct population of astroglial fusion-competent secretory vesicles.     

Prospects for applications of lanthanide-based upconverting surfaces to bioassay and detection

Biological assays to detect binding interactions are often conducted using fluorescence resonance energy transfer (FRET) but this has several disadvantages that markedly reduce the dynamic range of measurements. The very short range of FRET interactions also causes difficulties when large analytes such as viruses or spores are to be detected. Conventional FRET-based assays can in principle be improved using infrared-excited upconverting lanthanide-based energy donors but this does not address the short range of the FRET process. Here we investigate an alternative mode of energy transfer based on evanescent wave coupling from an erbium-doped waveguide to an absorbed fluorophore and characterise the luminescence from the dopant. The upconverted erbium emission is highly structured with well-separated bands in the violet, green and red spectral regions and very little detectable signal between the peaks. The relative intensity of these bands depends on power-density of infrared excitation. Green emission predominates at low power-density and red emission increases more rapidly as power-density increases, with a smaller violet peak also emerging. The temporal response of the upconverting material to pulsed infrared excitation was investigated and was shown to vary markedly with emission wavelength with the red component being particularly sensitive to the duration of the excitation pulse. A surface monolayer of the fluorescent protein R-phycoerythrin was very easily detected on binding to an upconverting waveguide. The potential advantages and limitations of the evanescent wave excitation technique for fluorescence detection are discussed and avenues for further development are considered.     

The translocation and post release settlement of red squirrels Sciurus vulgaris to a previously uninhabited woodland

Red squirrels have undergone a 30% contraction of their range in the last 10 years in Ireland, a decline attributed to the introduced grey squirrel. Large regions in the west of Ireland are free of both species of squirrel, due to the isolation of forests there and their relatively recent planting. The potential of these forests as translocation sites for red squirrels was investigated to ascertain the possibility of increasing the range of red squirrels in Ireland. Nineteen red squirrels were moved into Derryclare wood, Co. Galway using a soft release into enclosures, and their subsequent survival and settlement in the wood was monitored, using trapping and radio-tracking. The successful release of 94.7% of squirrels from the enclosure, and 68.4% survival to the start of the following year’s breeding season were in excess of the target survival rates of 75 and 50%, respectively. Five of the females were found to be lactating in May 2006, and seven offspring captured in August 2006. A squirrel was observed in a follow-up visit in October 2007. Radio-tracked red squirrels tended to remain in the general vicinity of release, incorporating supplementary feeders as part of their home ranges. Squirrels also fed on the natural food available in the wood, with feeding signs readily observed in the wider woodland. The techniques used proved very successful in survival, retention and future reproduction of the translocated population. Timing of release may be an important consideration for future translocations with survival better in summer-released animals.     

Acridine orange accumulation in acid organelles of normal and vacuolated frog skeletal muscle fibres

The spatial distribution of acid membrane organelles and their relationships with normal and vacuolated transverse tubules has been studied in living frog skeletal muscle fibres using confocal microscopy. Acridine orange (AO) was used to evaluate acid compartments, while a lipophilic styryl dye, RH 414, was employed to stain the membranes of the T-system. AO accumulated in numerous spherical granules located near the poles of nuclei and between myofibrils where they were arranged in short parallel rows, triplets or pairs. AO granules could be divided into three groups: green (monomeric AO), red (aggregated AO), and mixed green/red. As demonstrated by lambda-scanning, most granules were mixed. Double staining of muscle fibres with AO and RH 414 revealed almost all AO granules located near the transverse tubules. Vacuolation of the T-system was induced by glycerol loading and subsequent removal. The close juxtaposition of AO granules and the T-system was preserved in vacuolated fibres. The lumens of vacuoles did not accumulate AO. It is concluded that AO granules represent an accumulation of AO in lysosome-related organelles and fragmented Golgi apparatus and a possible functional role of the spatial distribution of such acidic compartments is discussed.     

Automatic cell identification and enrichment in lung cancer: V. Adenocarcinoma and large cell undifferentiated carcinoma

The aims of this study were to develop a protocol for the identification and enrichment of cancer cells from sputum obtained from patients with adenocarcinoma of the lung (n = 6) and large-cell undifferentiated carcinoma of the lung (n = 2), and to compare these findings with the results from our previous studies on other cell types from lung cancer. The hypotheses tested were: Cancer cells in sputum can be preserved following flow sorting. Enrichment for cancer cells from acridine orange (AO)-stained specimens can be achieved. Discrimination of cancer cells from noncancer cells is by AO green fluorescence and discrimination of lymphocytes from other cell types is by AO red fluorescence. Cancer cells are consistently enriched in the AO high green and red fluorescence region, although, for a given cell type, maximal enrichment is patient-dependent. Finally, cancer cell enrichment and lymphocyte exclusion can be done simultaneously. Cells from sputum were initially fixed, stained with AO, sorted on a dual parameter flow sorter, and classified into six groups corresponding to two ranges of green and three ranges of red fluorescence intensities. Cells of each region were stained by the method of Papanicolaou and differential counts were performed to determine the relative frequencies (i.e., purities) of leukocytes, macrophages, squamous cells, and cancer cells, in sorted and unsorted (i.e., control) samples. The average purity of leukocytes (81%), macrophages (6%), squamous cells (11%), and cancer cells (2%) varied markedly from sample to sample. However, the largest enrichment values (i.e., ratio of purity of a cell type in a sorted sample to its purity in the unsorted control sample) achieved for cancer cells consistently occurred for each patient sample in the region corresponding to high green and high red fluorescence intensities. Experimentally, a cancer cell average enrichment of sixteen-fold was obtained by this method. Additionally, fluorescence intensity ranges which increased the enrichment for macrophages by cell sorting typically excluded leukocytes and squamous cells, and vice versa. Finally, red fluorescence intensity was the primary discriminatory parameter for all cell types studied, although the additional use of green fluorescence intensity significantly increased cancer cell enrichment rates.(ABSTRACT TRUNCATED AT 400 WORDS)